public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) { ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl()); OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology); // reasoner.precomputeInferences(InferenceType.values()); long time = System.currentTimeMillis(); boolean isConsistent = reasoner.isConsistent(); int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size(); time = System.currentTimeMillis() - time; DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology)); String e = checker.getDescriptionLogicName(); String name = ontology.getOntologyID().getOntologyIRI().getFragment(); logger.info( "ontology: " + name + ", reasoner: " + factory.getReasonerName() + ", expressivity: " + e + ", consistent: " + isConsistent + ", unsat classes: " + numOfUnsatClasses + ", time: " + time); }
private void handleNotesOntologyChanged(List<OWLOntologyChange> changes) { try { OWLOntologyManager notesOntologyManager = notesOntology.getOWLOntologyManager(); if (notesOntologyManager.getOntologyFormat(notesOntology) instanceof BinaryOWLOntologyDocumentFormat) { OWLAPIProjectDocumentStore documentStore = OWLAPIProjectDocumentStore.getProjectDocumentStore(project.getProjectId()); List<OWLOntologyChangeData> infoList = new ArrayList<OWLOntologyChangeData>(); for (OWLOntologyChange change : changes) { OWLOntologyChangeRecord rec = change.getChangeRecord(); OWLOntologyChangeData info = rec.getData(); infoList.add(info); } BinaryOWLOntologyDocumentSerializer serializer = new BinaryOWLOntologyDocumentSerializer(); serializer.appendOntologyChanges( notesOntologyDocument, new OntologyChangeDataList(infoList, System.currentTimeMillis())); } else { // Swap it over notesOntologyManager.saveOntology(notesOntology, new BinaryOWLOntologyDocumentFormat()); } } catch (OWLOntologyStorageException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } }
protected OWLOntology loadBigOntology(String filename) { File file = new File(System.getenv("bigontosdir") + filename + ".owl"); OWLOntology ontology = null; try { ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(file); } catch (OWLOntologyCreationException e) { e .printStackTrace(); // To change body of catch statement use File | Settings | File // Templates. } return ontology; }
/** Serializes the A-box corresponding to a predicate into one or multiple file. */ private static void serializePredicate( OWLOntology ontology, Ontology inputOntology, OBDAModel obdaModel, Predicate predicate, String outputFile, String format) throws Exception { final long startTime = System.currentTimeMillis(); OWLAPI3Materializer materializer = new OWLAPI3Materializer(obdaModel, inputOntology, predicate, DO_STREAM_RESULTS); QuestOWLIndividualAxiomIterator iterator = materializer.getIterator(); System.err.println("Starts writing triples into files."); int tripleCount = 0; int fileCount = 0; String outputDir = outputFile; String filePrefix = Paths.get(outputDir, predicate.getName().replaceAll("[^a-zA-Z0-9]", "_") + "_").toString(); while (iterator.hasNext()) { tripleCount += serializeTripleBatch( ontology, iterator, filePrefix, predicate.getName(), fileCount, format); fileCount++; } System.out.println("NR of TRIPLES: " + tripleCount); System.out.println("VOCABULARY SIZE (NR of QUERIES): " + materializer.getVocabularySize()); final long endTime = System.currentTimeMillis(); final long time = endTime - startTime; System.out.println("Elapsed time to materialize: " + time + " {ms}"); }
public void runWithSingleFile() { BufferedOutputStream output = null; BufferedWriter writer = null; try { final long startTime = System.currentTimeMillis(); if (outputFile != null) { output = new BufferedOutputStream(new FileOutputStream(outputFile)); } else { output = new BufferedOutputStream(System.out); } writer = new BufferedWriter(new OutputStreamWriter(output, "UTF-8")); OBDAModel obdaModel = loadMappingFile(mappingFile); OWLOntology ontology = null; OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); OWLAPI3Materializer materializer = null; if (owlFile != null) { // Loading the OWL ontology from the file as with normal OWLReasoners ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile))); if (disableReasoning) { /* * when reasoning is disabled, we extract only the declaration assertions for the vocabulary */ ontology = extractDeclarations(manager, ontology); } Ontology onto = OWLAPI3TranslatorUtility.translate(ontology); obdaModel.declareAll(onto.getVocabulary()); materializer = new OWLAPI3Materializer(obdaModel, onto, DO_STREAM_RESULTS); } else { ontology = manager.createOntology(); materializer = new OWLAPI3Materializer(obdaModel, DO_STREAM_RESULTS); } // OBDAModelSynchronizer.declarePredicates(ontology, obdaModel); QuestOWLIndividualAxiomIterator iterator = materializer.getIterator(); while (iterator.hasNext()) manager.addAxiom(ontology, iterator.next()); OWLOntologyFormat ontologyFormat = getOntologyFormat(format); manager.saveOntology(ontology, ontologyFormat, new WriterDocumentTarget(writer)); System.err.println("NR of TRIPLES: " + materializer.getTriplesCount()); System.err.println("VOCABULARY SIZE (NR of QUERIES): " + materializer.getVocabularySize()); materializer.disconnect(); if (outputFile != null) output.close(); final long endTime = System.currentTimeMillis(); final long time = endTime - startTime; System.out.println("Elapsed time to materialize: " + time + " {ms}"); } catch (Exception e) { System.out.println("Error materializing ontology:"); e.printStackTrace(); } }